## Not run:
# # DONTRUN IS SET SO THIS IS NOT EXECUTED WHEN PACKAGE IS COMPILED - BUT THIS
# # HAS BEEN TESTED THOROUGHLY BEFORE UPLOADING TO THE REPOSITORY
#
# # Track the biomass of Pseudomonas over time, for 48 timepoints
# # with an output period of 1
# totalBiomass<-agent_getMeasureOverTime("/home/user/iDynoMiCS/results/",
# "agent_State", 48, 1, "Pseudomonas", "biomass")
#
# # Plot all the agents in the simulation at the 24th timestep
# plotAgents("/home/user/iDynoMiCS/results/", 24, "/home/user/iDynoMiCS/results")
#
# # Get the abundance of each species throughout a simulation of 48 timepoints
# # with an output period of 1
# speciesAbundance<-getSpeciesSpecificAbundance("/home/user/iDynoMiCS/results/",
# 48,1)
#
# # Plot the abundance of each species, 48 timepoints, output period of 1
# plotTimeCourseAgents("/home/user/iDynoMiCS/results/", 48, 1,
# "/home/user/Desktop/iDynoMiCS/results/single_species/graphs/")
#
# # Produce a diversity plot of this information, and store the data in the graph
# # 48 timepoints, output period of 1
# simpsonData<-simpsonIndex("/home/user/iDynoMiCS/results/", 48, 1,
# "/home/user/Desktop/iDynoMiCS/results/single_species/graphs/")
#
# # Get the total abundance of individuals throughout the simulation
# # 48 timepoints, output period of 1
# totalAbundance<-getSpeciesAbundance("/home/user/iDynoMiCS/results/", 48, 1)
#
# # Plot the total abundance. 48 timepoints, output period of 1
# plotTimeCourseAbund("/home/user/iDynoMiCS/results/", 48, 1,
# "/home/user/iDynoMiCS/results/graphs/")
#
# ## End(Not run)
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